plotomics 0.1.0

First release.

Fifteen GPU- and canvas-accelerated visualization widgets, built on a shared JavaScript core and exposed to R through htmlwidgets. Every widget renders in the RStudio Viewer, R Markdown, Quarto and Shiny, and every one ships a matching *Output() / render*() pair for classic Shiny apps.

Expression and abundance

• volcano() – differential expression, effect size against significance.
• bioheatmap() (alias heatmap_plotomics()) – large sample-by-gene matrices. Named to avoid masking stats::heatmap().
• clustermap() – expression matrix with row and column dendrograms.
• dotplot() – marker genes by group, dot area for the fraction expressing and colour for the level.
• violin() – one row per feature, one violin per group. violin_density() computes the densities in R.

Single-cell and spatial

• embedding() – UMAP, t-SNE and PCA scatter at several hundred thousand points. A factor color column pins the legend order and keeps unused levels, the way drop = FALSE does in ggplot2.
• spatial() – measurements at their slide coordinates over the histology image, with image and spots sharing one fit so they cannot drift apart on resize.

Cohort and variant genomics

• oncoplot() – the cohort alteration landscape, with mutation-burden and per-gene frequency barplots and clinical annotation strips. oncoplot_memo_sort() produces the conventional column order.
• lollipop() – variants along a protein over its domain architecture.
• km() – Kaplan-Meier curves with censoring ticks, confidence bands and a number-at-risk table. Accepts a survival::survfit object directly.
• bioprofile() – grouped categorical profile, built for the 96-context mutational signature layout.

Sets, hierarchies and networks

• upset() – set intersections for the many-set case. upset_intersections() computes exclusive intersections, so columns sum to the union rather than double-counting.
• treemap() – hierarchical gene-set and pathway composition.
• network() – large biological networks, with directed edges, per-edge colour and node-click selection that pushes the clicked id to input$<outputId>_selected in Shiny.

Genome and chromatin

• hic() – Hi-C contact matrices with level-of-detail tiling.